/EXTERNAL McGill EMC/variants/K006150_1_lane_gembs
BACK
SAMPLE K006150_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1144999124 |
643062284 |
56.16 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1144999124 |
100% |
1133436729 |
98.99 % |
11562395 |
1.01 % |
| |
|
|
|
|
|
|
| Passed |
645053635 |
56.34 % |
641218123 |
56.57 % |
3835512 |
0.59 % |
| Filtered |
499945489 |
43.66 % |
492218606 |
43.43 % |
7726883 |
1.20 % |
| |
|
|
|
|
|
|
| q20 |
465651016 |
93.14 % |
463828354 |
94.23 % |
1822662 |
23.59 % |
| q20,qd2 |
14438339 |
2.89 % |
8917446 |
1.81 % |
5520893 |
71.45 % |
| q20,mq40 |
12513727 |
2.50 % |
12424419 |
2.52 % |
89308 |
1.16 % |
| q20,qd2,mq40 |
3103727 |
0.62 % |
3001728 |
0.61 % |
101999 |
1.32 % |
| qd2 |
2569850 |
0.51 % |
2521448 |
0.51 % |
48402 |
0.63 % |
| mq40 |
1622533 |
0.32 % |
1488585 |
0.30 % |
133948 |
1.73 % |
| qd2,mq40 |
44545 |
0.01 % |
36626 |
0.01 % |
7919 |
0.10 % |
| qd2,fs60,mq40 |
731 |
0.00 % |
0 |
0.00 % |
731 |
0.01 % |
| qd2,fs60 |
337 |
0.00 % |
0 |
0.00 % |
337 |
0.00 % |
| fs60,mq40 |
244 |
0.00 % |
0 |
0.00 % |
244 |
0.00 % |
| fs60 |
215 |
0.00 % |
0 |
0.00 % |
215 |
0.00 % |
| q20,qd2,fs60 |
131 |
0.00 % |
0 |
0.00 % |
131 |
0.00 % |
| q20,qd2,fs60,mq40 |
94 |
0.00 % |
0 |
0.00 % |
94 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
Coverage and Quality
| Coverage Variants |
Quality Variants |
 |
 |
Filtering Criteria Distribution
| Phred scale strand bias estimated using Fisher's Exact Test. |
 |
| Allele-specific call confidence normalized by depth of sample reads supporting the allele. Variants. |
Allele-specific call confidence normalized by depth of sample reads supporting the allele. Non-Variants. |
 |
 |
| Root Mean Square of the mapping quality of reads. Variants. |
Root Mean Square of the mapping quality of reads. Non-Variants. |
 |
 |
Mutations
| Type |
Mutation |
Status |
# |
% |
| Transition |
A>G |
All |
3938667 |
29.70 % |
| Transition |
G>A |
All |
989643 |
7.46 % |
| Transition |
T>C |
All |
3382220 |
25.51 % |
| Transition |
C>T |
All |
1026139 |
7.74 % |
| Transversion |
A>C |
All |
251748 |
1.90 % |
| Transversion |
C>A |
All |
1084270 |
8.18 % |
| Transversion |
T>G |
All |
281792 |
2.13 % |
| Transversion |
G>T |
All |
1067229 |
8.05 % |
| Transversion |
A>T |
All |
353276 |
2.66 % |
| Transversion |
T>A |
All |
371140 |
2.80 % |
| Transversion |
C>G |
All |
267679 |
2.02 % |
| Transversion |
G>C |
All |
246789 |
1.86 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
428564 |
16.76 % |
| Transition |
G>A |
Passed |
403596 |
15.78 % |
| Transition |
T>C |
Passed |
430548 |
16.84 % |
| Transition |
C>T |
Passed |
409922 |
16.03 % |
| Transversion |
A>C |
Passed |
110648 |
4.33 % |
| Transversion |
C>A |
Passed |
118414 |
4.63 % |
| Transversion |
T>G |
Passed |
110738 |
4.33 % |
| Transversion |
G>T |
Passed |
117256 |
4.59 % |
| Transversion |
A>T |
Passed |
100384 |
3.93 % |
| Transversion |
T>A |
Passed |
100445 |
3.93 % |
| Transversion |
C>G |
Passed |
113017 |
4.42 % |
| Transversion |
G>C |
Passed |
113424 |
4.44 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPAll |
0 |
0.00 % |
| Transition |
G>A |
dbSNPAll |
0 |
0.00 % |
| Transition |
T>C |
dbSNPAll |
0 |
0.00 % |
| Transition |
C>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPAll |
0 |
0.00 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPPassed |
0 |
0.00 % |
| Transition |
G>A |
dbSNPPassed |
0 |
0.00 % |
| Transition |
T>C |
dbSNPPassed |
0 |
0.00 % |
| Transition |
C>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPPassed |
0 |
0.00 % |
| |
|
|
|
|
Ti/Tv Ratio
| Status |
Ratio |
Transitions |
Transversions |
| All |
2.38 |
9336669 |
3923923 |
| Passed |
1.89 |
1672630 |
884326 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |